IVT RNA cleaved and ligated with splint A to select 18 nt deletion, replicate 1
Edited IVT RNA of SARS-CoV-2 N gene was sequenced using Oxford Nanopore with Ligation Sequencing Kit (SQK-LSK109). RNA was reverse transcribed using LunaScript RT SuperMix Kit (NEB), and cDNA was used for PCR with primers nCoV-96_L/nCoV-96_R (Table S4) and Q5 polymerase (NEB). DNA was purified using magnetic beads (Omega Bio-tek, M1378-01) and used to prepare sequencing libraries as described in SQK-LSK109 protocol using Native Barcoding Expansion 1-12 (EXP-NBD104). Resulting library (~20 ng) was sequenced on the Nanopore MinION with R9.4.1 flow cell. The sequencing run was performed in the high-accuracy base calling mode in the MinKNOW software.